Model Organisms and Ciona intestinalis
Many of the model organisms used in science to better understand human anatomy and physiology are largely unknown to the general public. Or we still know them from biology textbooks and didn’t think much further about them.
Ciona intestinalis, sea squirt or vase tunicate, is one such organism. It is used for research into the embryonic development of the circulatory system, the heart and blood vessels, and for research on the development of nerves. Much research on Ciona is done on the larvae, but the adult animal is also interesting. The nervous system is clearly visible through the transparent body and can therefore be studied well in vivo. An adult sea squirt also has an organ comparable to our thyroid gland, the endostyle.
In many biology books, you can find descriptions and illustrations of the translucent vase tunicate as an example of a primitive chordate. Chordates are bilaterally symmetrical, have a coelom or abdominal cavity, and a closed circulatory system. The notochord (chorda), a flexible rod-like organ in the back of an animal, is often only visible in the larval stage. These illustrations are often simplified to clarify how the different structures fit together. This makes sense; if you put too much into an illustration, it becomes cluttered, but the danger is that along the way, as illustrations are often copied from older illustrations, information is lost. So, to make a good anatomical 3D model of a Ciona intestinalis, you really need to have good references.
Gathering References and Information
In this article, I describe how I modeled the anatomy of an adult vase tunicate. First, of course, I try to get hold of the animal itself. In this case, that is not really possible because I do not live by the sea and sea squirts are not eaten. Therefore I looked up a lot of photos and watched videos of the animal in its natural environment. So unfortunately, a dissection was not in the cards for this animal.
Furthermore, I naturally looked at all available illustrations. Those two combined, along with my own anatomical and taxonomic knowledge, gave me a foundation to dive into the literature.
Like all animals, a vase tunicate naturally has a circulatory system, heart, and blood vessels (Hoshino, 1969), a nervous system and a central ganglion/ganglia (Osugi et al., 2017), a digestive system (Carver et al., n.d.), and a reproductive system (Carver et al., n.d.). So, I started looking for those in the literature using the right keywords. What I always notice when I do this is that I slowly discover more and more that absolutely cannot be missing from the final anatomical model. For instance, the endostyle (Thorpe, 1972) is visualized in detail in hardly any illustration, except as a long structure on the ventral side of the animal, even though it is a very intriguing organ with a very clear segmentation. But I found a great reference.
An infographic made with the final anatomical 3d model of Ciona intestinalis
The Modeling Process
As soon as I have a rough idea of the various organ systems, I start modeling. In doing so, I always make sure to start with a structure to which I can ‘hang’ the rest. In vertebrates, for example, this is the skeleton; in a sea squirt, it is the tunic (mantle). I already think about how the other systems need to fit in there from a technical standpoint and ensure a mesh that can be easily modified. Because everything is related to this, I spend a relatively large amount of work on it, even though the final result looks relatively simple. For Ciona, I have to at least ensure that the blood vessels and nerves can run through the wall of the tunic and that the cavities for the organs are correct. I had the most trouble with the atrial cavity coupled with the atrial siphon. This is mainly because many structures open into it: the digestive tract runs far along the wall of the branchial basket, but the oviduct and sperm duct run there as well. And the branchial basket has its own cavity that sits within the atrial cavity. The atrial cavity is separated from the coelom (abdominal cavity) by means of a septum.
A realistic rendition of the finished 3d model in Marmoset Toolbag
Once I had that mesh right, I could start on the rest. The most striking structure is, of course, the branchial basket. Shaping it in such a way that it has a visual representation people understand, that it fits within the structure, that all connections are correct, and so that the model will have an acceptable size later on—that is not easy. Within the structure of the branchial basket run blood vessels, which absorb oxygen from the water via the gill slits, and nerves. Furthermore, the branchial basket is connected to the short esophagus that leads to the stomach. And that stomach, in turn, lies in the abdominal cavity (coelom). The entire digestive tract must, of course, have seamless connections so that it is visually a whole, but because the model will ultimately be used in an application, those parts must also be separate.
The same goes for the circulatory system: the heart lies in a pericardium (Waldrop and Miller, 2015) and is partially connected to that same pericardium. The large blood vessels lie on the dorsal and ventral sides of the branchial basket, and horizontal blood vessels around that basket connect those two large blood vessels. The circulatory system also works differently than you would expect in an animal with a heart and a closed system: the direction in which the blood flows reverses periodically (Waldrop and Miller, 2015). The large ventral vessel lies against the endostyle, so those two had to remain running parallel. However, the endostyle lies within the branchial cavity and is connected to the branchial basket. Yet, the endostyle continues for a bit underneath the branchial basket, and therefore the branchial cavity does too.
The endostyle consists of eight epithelial zones that are largely the same over the entire length of the endostyle (Thorpe, 1972). But because it curves and has these distinct structures, here too it took some figuring out how to ensure that the structures remained visible while keeping the object at an acceptable size.
Once those structures were made, the reproductive system was quite manageable. Ciona is a hermaphrodite, so it has both an ovary and a testis (Okada and Yamamoto, 1999). Both are single. The testis lies as branched tubules on top of the large mass of the ovary. A tube runs from both towards the atrial siphon. The oviduct stops earlier than the sperm duct.
After I made these organs, I took care of the longitudinal muscles. These run from the location where the attachments sit for anchoring to a solid substrate up into the ends of both siphons, where they branch. This allows the sea squirt to move its entire structure.
The nervous system of Ciona (Osugi et al., 2017) is still fairly complex, and it took me time to gather the right information. Just like with the other structures, it involves digging into the literature (Mackie, 1995). The dorsal strand complex is especially interesting because it actually influences all organs. This involves a network of neurons in the wall of the viscera. This network has both sensory and motor properties. The neural gland is also part of the nervous system; the gland lies directly against the rudimentary brain (cerebral ganglion).
Above, I describe the most important aspects of the anatomy. While making this model, which is of course relatively simple, I mainly ran into the fact that it is not a vertebrate. The available information is hidden deep within research; it is really a matter of searching to find the correct data. Sometimes data also contradict each other. I would then look at the ‘status’ of an article and see if I could find confirmation of the data found. That, of course, is still uncertain, especially when there is very little confirmation. If I could not find confirmation, the structure did not end up in the model.
A screenshot of the app where the anatomical 3d model of Ciona intestinalis is added.
A screenshot of the app with a view on the dorsal strand complex
The finished 3d model of Ciona intestinalis. Ready to be implemented into an app.
Future Outlook and Optimization
Am I finished with this model now? Not really. What I have made now is the foundation. I am fairly certain that it will be worked on over the coming years, that I will adjust structures, and above all, that I will add more detail. For now, you mainly see the coarse structures that make the anatomy of the translucent sea squirt understandable for students. But with digital 3D, you are not limited to just the coarse structures.
The resulting model is now 30 MB. That is more than enough to run smoothly in an online application. I have optimized the model to a certain extent, but if extra details make the model much larger, that optimization can go much further, precisely without losing details again. It is a matter of using the right format and choosing what goes where. Sometimes it is better to just create a mesh; sometimes you can use textures instead to introduce details.
However, I would most like to model the entire developmental lineage from early embryo to adult sea squirt. Even that can be developed in a way that can be used in an application. To develop such a lineage, I would have to model various developmental moments and bridge the intermediate phases using shape keys. If you have such a model, you can show the development of a translucent sea squirt as a 4D animation, which makes gaining an understanding of the anatomy and how it develops over time a lot more fun.
Models like these provide a highly accessible view of the anatomy of unknown animals that are nevertheless so important for scientific research for the benefit of humans.
References
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